WO2016018481A3 - Stratification de mutations tumorales basée sur des réseaux - Google Patents

Stratification de mutations tumorales basée sur des réseaux Download PDF

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Publication number
WO2016018481A3
WO2016018481A3 PCT/US2015/028343 US2015028343W WO2016018481A3 WO 2016018481 A3 WO2016018481 A3 WO 2016018481A3 US 2015028343 W US2015028343 W US 2015028343W WO 2016018481 A3 WO2016018481 A3 WO 2016018481A3
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WO
WIPO (PCT)
Prior art keywords
network based
tumor mutations
based stratification
stratification
subject
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2015/028343
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English (en)
Other versions
WO2016018481A2 (fr
Inventor
Trey Ideker
Matan HOFREE
John Paul Shen
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of California Berkeley
University of California San Diego UCSD
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University of California Berkeley
University of California San Diego UCSD
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Application filed by University of California Berkeley, University of California San Diego UCSD filed Critical University of California Berkeley
Publication of WO2016018481A2 publication Critical patent/WO2016018481A2/fr
Publication of WO2016018481A3 publication Critical patent/WO2016018481A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Analytical Chemistry (AREA)
  • Databases & Information Systems (AREA)
  • Organic Chemistry (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Oncology (AREA)
  • Microbiology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Les modes de réalisation de l'invention concernent un procédé de stratification d'un cancer en un ou plusieurs sous-types informatifs chez un sujet en ayant besoin. Les modes de réalisation concernent en outre l'association d'un sujet en ayant besoin à un ou plusieurs sous-types informatifs, notamment l'association d'un sujet en ayant besoin à un sous-type informatif, ce sous-type étant un sous-type de cancer de l'ovaire.
PCT/US2015/028343 2014-07-28 2015-04-29 Stratification de mutations tumorales basée sur des réseaux Ceased WO2016018481A2 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201462029868P 2014-07-28 2014-07-28
US62/029,868 2014-07-28

Publications (2)

Publication Number Publication Date
WO2016018481A2 WO2016018481A2 (fr) 2016-02-04
WO2016018481A3 true WO2016018481A3 (fr) 2016-03-03

Family

ID=55218434

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2015/028343 Ceased WO2016018481A2 (fr) 2014-07-28 2015-04-29 Stratification de mutations tumorales basée sur des réseaux

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WO (1) WO2016018481A2 (fr)

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109196121B (zh) 2016-02-29 2022-01-04 基因泰克公司 用于癌症的治疗和诊断方法
CN109476731A (zh) 2016-02-29 2019-03-15 基础医药有限公司 治疗癌症的方法
JP6930992B2 (ja) * 2016-02-29 2021-09-01 ファウンデーション・メディシン・インコーポレイテッド 腫瘍変異負荷を評価するための方法及びシステム
WO2017220782A1 (fr) * 2016-06-24 2017-12-28 Molecular Health Gmbh Procédé de dépistage du cancer de l'endomètre
EP3523451A1 (fr) 2016-10-06 2019-08-14 Genentech, Inc. Méthodes thérapeutiques et de diagnostic du cancer
US20180203974A1 (en) * 2016-11-07 2018-07-19 Grail, Inc. Methods of identifying somatic mutational signatures for early cancer detection
EP3631003A4 (fr) * 2017-06-01 2021-03-10 NantOmics, LLC Étude de l'hétérogénéité tumorale et temporelle par profilage exhaustif par approches "omiques" chez les patientes atteintes d'un cancer du sein métastatique triple négatif
EP3655034A1 (fr) 2017-07-21 2020-05-27 Genentech, Inc. Procédés thérapeutiques et de diagnostic du cancer
EP3728642A4 (fr) * 2017-12-18 2021-09-15 Personal Genome Diagnostics Inc. Système d'apprentissage automatique et procédé de découverte de mutations somatiques
US11887698B2 (en) * 2020-01-08 2024-01-30 Samsung Electronics Co., Ltd. Method and electronic device for building comprehensive genome scale metabolic model
WO2022244006A1 (fr) * 2021-05-19 2022-11-24 Ramot At Tel-Aviv University Ltd. Classification et pronostic du cancer reposant sur des mutations silencieuses et non silencieuses
CN113736790B (zh) * 2021-10-14 2023-05-02 四川农业大学 一种敲除鸭hnRNPA3基因的sgRNA、细胞系及其构建方法和应用
WO2023173023A1 (fr) * 2022-03-10 2023-09-14 Lantern Pharma Inc. Systèmes et procédés informatisés de découverte de médicament basée sur un modèle ensembliste
CN114972163B (zh) * 2022-03-15 2025-02-18 常州桐树生物科技有限公司 基于图卷积神经网络识别微卫星不稳定性状态的方法
CN115966316B (zh) * 2023-02-10 2023-07-04 北京大学 肿瘤药物敏感性预测方法、系统、设备及存储介质
WO2025178968A2 (fr) * 2024-02-21 2025-08-28 The Regents Of The University Of California Variants fonctionnels non codants utilisés en tant que biomarqueurs du cancer

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
AVESSON ET AL.: "The emerging role of RNA and DNA editing in cancer", BIOCHEM BIOPHYS ACTA, vol. 1845, no. 2, pages 308 - 316 *
DATABASE GenBank [o] 14 November 2006 (2006-11-14), "Homo sapiens partial TTN gene for titin", Database accession no. AJ277892.2 *
DATABASE UNIPROT [o] 9 July 2014 (2014-07-09), "Titin human.", Database accession no. Q8WZ42. *
GREENMAN ET AL.: "Patterns of somatic mutation in human cancer genomes.", NATURE, vol. 446, no. 7132, 8 March 2007 (2007-03-08), pages 153 - 158, XP055155126, DOI: doi:10.1038/nature05610 *
HOFREE ET AL.: "Network-based stratification of tumor mutations.", NATURE METHODS, vol. 10, no. 11, 5 September 2013 (2013-09-05), pages 1108 - 1115, XP055193269, DOI: doi:10.1038/nmeth.2651 *
KARVE ET AL.: "Small changes huge impact: the role of protein posttranslational modifications in cellular homeostasis and disease", J AMINO ACIDS, vol. 2011, no. 207691, pages 1 - 13 *

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Publication number Publication date
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